The first episode didn't retcon the mythology, the nature of the mythology was just modified and reversed. Aliens are still real (there's no way humans could have engineered complex entities like the black oil, greys and the faceless rebels), Mulder and Scully were still talking about the implications of alien DNA in tonight's episode it's just that...
Before:
-Aliens are real, they're basically very bad because they want to colonize the earth and either wipe out or subjugate humanity.
-The syndicate is the lesser of two evils, they do terrible things and are murderers but they were trying to buy time so at least some of humanity can survive (well, maybe mostly themselves and their own families).
After:
-Aliens are real but their interest in visiting the earth was instigated by the first nuclear tests and some kind of concern for humanity (how genuine that concern really was, who knows), not enslavement and exploitation.
-People like the syndicate are the real evil, they have killed innocent aliens like the Roswell survivor ruthlessly and are using alien technology in order to ultimately enslave humanity.
So basically, unless I'm missing something it boils down to the syndicate and whoever has apparently replaced them along with survivors like CSM are the ones who actually wanted to enslave humanity all along, not the aliens.
Whatever happens I'm thinking the Tad O'Malley story at least gets turned on its ear in some way during the finale.
Still makes no sense. There are tons of scenes in the original run between Syndicate members talking about colonization and the like and they'd have no reason to continue the ruse in their private meetings unless they were all major LARPers.